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- PDB-1ep3: CRYSTAL STRUCTURE OF LACTOCOCCUS LACTIS DIHYDROOROTATE DEHYDROGEN... -

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Basic information

Entry
Database: PDB / ID: 1ep3
TitleCRYSTAL STRUCTURE OF LACTOCOCCUS LACTIS DIHYDROOROTATE DEHYDROGENASE B. DATA COLLECTED UNDER CRYOGENIC CONDITIONS.
Components(DIHYDROOROTATE DEHYDROGENASE B ...) x 2
KeywordsOXIDOREDUCTASE / Heterotetramer / ALPHA-BETA barrel / BETA sandwich / FAD domain / ALPHA/BETA NADP domain / FeS cluster binding domain
Function / homology
Function and homology information


dihydroorotate dehydrogenase (NAD+) / dihydroorotate dehydrogenase (NAD+) activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / electron transfer activity / oxidoreductase activity / metal ion binding / cytoplasm
Similarity search - Function
Dihydroorotate dehydrogenase B (pyrk subunit); domain 3 / Dihydroorotate dehydrogenase, electron transfer subunit / Dihydroorotate dehydrogenase electron transfer subunit / Dihydroorotate dehydrogenase, class 1B / Dihydroorotate dehydrogenase, electron transfer subunit, Fe-S binding domain superfamily / : / Cytochrome-c3 hydrogenase, gamma subunit / Dihydroorotate dehydrogenase, electron transfer subunit, iron-sulphur cluster binding domain / : / Iron-sulfur cluster binding domain of dihydroorotate dehydrogenase B ...Dihydroorotate dehydrogenase B (pyrk subunit); domain 3 / Dihydroorotate dehydrogenase, electron transfer subunit / Dihydroorotate dehydrogenase electron transfer subunit / Dihydroorotate dehydrogenase, class 1B / Dihydroorotate dehydrogenase, electron transfer subunit, Fe-S binding domain superfamily / : / Cytochrome-c3 hydrogenase, gamma subunit / Dihydroorotate dehydrogenase, electron transfer subunit, iron-sulphur cluster binding domain / : / Iron-sulfur cluster binding domain of dihydroorotate dehydrogenase B / Dihydroorotate dehydrogenase, class 1 / Dihydroorotate dehydrogenase, class 1/ 2 / Dihydroorotate dehydrogenase signature 1. / Dihydroorotate dehydrogenase signature 2. / Dihydroorotate dehydrogenase, conserved site / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / : / Dihydroorotate dehydrogenase domain / Dihydroorotate dehydrogenase / Translation factors / Elongation Factor Tu (Ef-tu); domain 3 / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Ribbon / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / Dihydroorotate dehydrogenase B (NAD(+)), catalytic subunit / Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit
Similarity search - Component
Biological speciesLactococcus lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRowland, P. / Norager, S. / Jensen, K.F. / Larsen, S.
Citation
Journal: Structure Fold.Des. / Year: 2000
Title: Structure of dihydroorotate dehydrogenase B: electron transfer between two flavin groups bridged by an iron-sulphur cluster.
Authors: Rowland, P. / Norager, S. / Jensen, K.F. / Larsen, S.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1997
Title: Crystallization and Preliminary X-ray Diffraction Analysis of the Heterotetrameric Dihydroorotate Dehydrogenase B of Lactococcus lactis, a Flavoprotein Enzyme System Consisting of two PyrDB ...Title: Crystallization and Preliminary X-ray Diffraction Analysis of the Heterotetrameric Dihydroorotate Dehydrogenase B of Lactococcus lactis, a Flavoprotein Enzyme System Consisting of two PyrDB Subunits and Two Iron-Sulfur Cluster Containing PyrK Subunits
Authors: Rowland, P. / Nielsen, F.S. / Jensen, K.F. / Larsen, S.
#2: Journal: J.Biol.Chem. / Year: 1996
Title: The B Form of Dihydroorotate Dehydrogenase from Lactococcus lactis Consists of two Different Subunits, Encoded by the pyrDb and PyrK Genes, and Contains FMN, FAD and [FeS] Redox Centers
Authors: Nielsen, F.S. / Andersen, P.S. / Jensen, K.F.
#3: Journal: Flavins and Flavoproteins / Year: 1999
Title: Roles of three prosthetic groups in tetrameric Dihydroorotate dehydrogenase B from Lactococcus lactis
Authors: Jensen, K.F. / Bjornberg, O. / Nielsen, F.S. / Ottosen, M. / Sorensen, P.G. / Rowland, P. / Norager, S. / Larsen, S.
History
DepositionMar 27, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DIHYDROOROTATE DEHYDROGENASE B (PYRD SUBUNIT)
B: DIHYDROOROTATE DEHYDROGENASE B (PYRK SUBUNIT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0855
Polymers61,6682
Non-polymers1,4183
Water8,395466
1
A: DIHYDROOROTATE DEHYDROGENASE B (PYRD SUBUNIT)
B: DIHYDROOROTATE DEHYDROGENASE B (PYRK SUBUNIT)
hetero molecules

A: DIHYDROOROTATE DEHYDROGENASE B (PYRD SUBUNIT)
B: DIHYDROOROTATE DEHYDROGENASE B (PYRK SUBUNIT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,17110
Polymers123,3354
Non-polymers2,8356
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_676x-y+1,-y+2,-z+11
Buried area13990 Å2
ΔGint-110 kcal/mol
Surface area41350 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)199.89, 199.89, 80.27
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-578-

HOH

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Components

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DIHYDROOROTATE DEHYDROGENASE B ... , 2 types, 2 molecules AB

#1: Protein DIHYDROOROTATE DEHYDROGENASE B (PYRD SUBUNIT)


Mass: 32977.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: P54322, EC: 1.3.3.1
#2: Protein DIHYDROOROTATE DEHYDROGENASE B (PYRK SUBUNIT)


Mass: 28690.295 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: P56968, EC: 1.3.3.1

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Non-polymers , 4 types, 469 molecules

#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 466 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 2.1 - 2.4 M Ammonium sulfate, 0.1 M Na-acetate pH 4 to 5, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 6
Details: Rowland, P., (1997) Acta Crystallogr., Sect.D, 53, 802.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
250 mMsodium phosphate1drop
310 %glycerol1drop
42.4 Mammonium sulfate1reservoir
50.1 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8469
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 26, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8469 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 270295 / Num. obs: 35821 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 17.5 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 16.62
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 0.327 / Num. unique all: 1554 / % possible all: 87.5
Reflection
*PLUS
Num. measured all: 270295

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1EP1

1ep1


Resolution: 2.1→20 Å / Rfactor Rfree error: 0.004 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.237 3509 10 %RANDOM
Rwork0.195 ---
all-35305 --
obs-35305 98.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 79.1266 Å2 / ksol: 0.374949 e/Å3
Displacement parametersBiso mean: 32.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4300 0 88 466 4854
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009084
X-RAY DIFFRACTIONc_angle_deg1.42637
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d1.13892
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.295 584 10.3 %
Rwork0.251 5106 -
obs--96 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.195
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 32.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.13892
LS refinement shell
*PLUS
Rfactor Rfree: 0.295 / % reflection Rfree: 10.3 % / Rfactor Rwork: 0.251

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